Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Identifying critical period of type 2 diabetes in Chinese population with leading molecules based on dynamic network biomarkers.

Scientific reports·2026

Same author

Towards the construction of a virtual yeast.

Nature·2026

Same author

Disruption of dynactin complex function in intellectual disability.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Efficient preservation of old methane-derived organic carbon in deep-sea surface sediments.

Nature communications·2026

Same author

CauFinder: Steering Cell-State and Phenotype Transitions by Causal Disentanglement Learning.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026

Same author

stMixer for Scalable Mosaic Integration and Label Transfer in Spatial Histology and Multi-Omics.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026

Same journal

Cap 2'-O-methyltransferase CMTR2 regulates male meiosis independent of its methyltransferase activity.

Nucleic acids research·2026

Same journal

APE1 binds and processes abasic sites present in i-motif DNA and cooperates with PCBP1 in maintenance of telomeric stability.

Nucleic acids research·2026

Same journal

Acquisition of a novel restriction modification system regulates genetic flux and gene expression in the hypervirulent and globally disseminated CC17 lineage of group B Streptococcus.

Nucleic acids research·2026

Same journal

Trans-species microRNAs from the parasitic plant Cuscuta campestris specifically avoid loading onto self Argonautes.

Nucleic acids research·2026

Same journal

Neurochondrin promotes U5 snRNP maturation by regulating AAR2 release from PRPF8.

Nucleic acids research·2026

Same journal

Elongationless start-stop elements are stress-resilient translation gates that are more repressive than uTranslons.

Nucleic acids research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 10, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Dual decoding of cell types and gene expression in spatial transcriptomics with PANDA.

Meng-Guo Wang¹, Luonan Chen^2,3,4, Xiao-Fei Zhang^1,5

¹School of Mathematics and Statistics, and Hubei Key Lab-Math. Sci., Central China Normal University, Wuhan 430079, Hubei, China.

Nucleic Acids Research

|October 15, 2024

Summary

This summary is machine-generated.

PANDA is a new computational method that deconvolutes spatial transcriptomics data to reveal cell type proportions and cell-type-specific gene expression. This approach uncovers hidden cellular heterogeneity within tissues, improving our understanding of complex biological systems.

More Related Videos

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level

Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level

Published on: March 14, 2022

Related Experiment Videos

Last Updated: Jun 10, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level

Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level

Published on: March 14, 2022

Area of Science:

Genomics
Computational Biology
Molecular Biology

Background:

Spatial transcriptomics enables transcriptome profiling with spatial context.
Spot-level data often mixes signals from multiple cells, masking heterogeneity.
Current deconvolution methods focus on cell proportions but miss cell-type-specific expression.

Purpose of the Study:

To develop a novel method for deconvoluting spatial transcriptomics data.
To simultaneously identify cell type proportions and cell-type-specific gene expression per spot.
To capture and analyze intra-type heterogeneity within spatial transcriptomics data.

Main Methods:

Developed PANDA (Probabilistic-based deconvolution with spot-adaptive cell type signatures).
Integrated archetypal analysis to capture within-cell-type heterogeneity.
Dynamically learned cell type signatures for each spot during deconvolution.

Main Results:

PANDA demonstrated superior performance in simulations compared to existing methods.
Applied to tumor, brain, and heart tissues, PANDA accurately reconstructed spatial structures.
Revealed subtle transcriptional variations within specific cell types, offering deeper biological insights.

Conclusions:

PANDA provides a comprehensive approach to spatial transcriptomics data analysis.
The method enhances the understanding of tissue dynamics by resolving cellular heterogeneity.
PANDA facilitates a more nuanced interpretation of gene expression in complex biological systems.